CellMigPCAclustALL {cellmigRation} | R Documentation |
The CellMigPCAclust function automatically generates clusters based on the Principal Component Analysis.
CellMigPCAclustALL( object, ExpName = "PCA_Clusters", parameters = c(1, 2, 3), export = FALSE, interactive = TRUE )
object |
|
ExpName |
A character string. The ExpName will be appended to all exported tracks and statistics data. |
parameters |
A numeric vector contains the parameters to be included in the Principal Component Analysis. These numbers can be obtained from the outcome of the FinRes() function. |
export |
if 'TRUE' (default), exports function output to CSV file |
interactive |
logical, shall the PCA analysis be generated in a interactive fashion |
PCA Graph of cells and PCA Graph of variables.
Salim Ghannoum salim.ghannoum@medisin.uio.no
https://www.data-pulse.com/dev_site/cellmigration/
## The analysis only supports the interactive method! ## If interactive=FALSE, the function will return NULL data(WSADataset) wasDF1 <- WSADataset[seq(1,300,by=1), ] wsaTD1 <- CellMig(wasDF1) wsaTD1 <- wsaPreProcessing(wsaTD1,FrameN=55) wsaTD1 <-FMI(wsaTD1,TimeInterval=10) wsaTD1 <-FinRes(wsaTD1,ParCor=FALSE, export=FALSE) wasDF2 <- WSADataset[seq(500,700,by=1), ] wsaTD2 <- CellMig(wasDF2) wsaTD2 <- wsaPreProcessing(wsaTD2,FrameN=55) wsaTD2 <-FMI(wsaTD2, TimeInterval=10) wsaTD2 <-FinRes(wsaTD2, ParCor=FALSE, export=FALSE) AGG <- aggregateFR(wsaTD1, wsaTD2, export=FALSE) CellMigPCAclustALL(AGG,ExpName="Aggregated_Conditions", parameters=c(1,6), export=FALSE, interactive=FALSE) # The previous line returns NULL # In an interactive session, try running the following command (uncomment!) # CellMigPCAclustALL(AGG,ExpName="Aggregated_Conditions", # parameters=c(1,6), export=FALSE)